Doctoral INPhINIT Fellowships Programme - Incoming. Call for applications 2022.

Application submission deadline: 27/01/2022
The Gene Regulation of Cell Identity lab is looking for outstanding candidates to apply for an Inphinit doctoral fellowship to join the lab. The selected candidate will work in a project aimed at understanding the function of RNA Binding Proteins in the control of Gene Regulatory Networks in single cells. Interested candidates please contact Dr. Plass for further details.

Position description

Research Project / Research Group Description
The Regulation of Cell Identity Group is a multidisciplinary young research group that started at the end of 2019 at the Program of Regenerative Medicine (P-CMRC) at the Bellvitge Biomedical Research Institute (IDIBELL). In the lab we are interested in understanding how gene regulation is involved in the definition of cell types and how changes in this regulation are altered during the development of neurodegenerative diseases. In particular, we are interested in understanding which is the contribution of RNA Binding Proteins (RBPs) to this process. RBPs are the key orchestrators of gene regulation at the post-transcriptional level. These proteins control several mechanisms such as splicing, polyadenylation, translation and mRNA decay that are essential for defining the final transcript and protein repertoire in a cell. Yet, there is not much knowledge about how these RBPs contribute to the definition of cell types or how alterations in the expression or the function of these RBPs contributes to cause disease states.
To investigate these questions, we use a multidisciplinary approach combining molecular and cellular biology approaches, high-throughput sequencing technologies and computational analyses. We are using induced pluripotent stem cells (iPSCs) to study the changes in gene expression that exist during the differentiation of neural cell types in vitro and study the dynamics of RBP expression. By comparing these dynamics to those from patient-derived iPSCs, we aim at understanding the importance of RNA processing in the development of Alzheimer and other neurodegenerative diseases.
Job position description
The mechanisms that define cell identity in complex organisms are still largely unknown. Most efforts have been focused on understanding how transcription factors (TFs) direct cell differentiation such as during development or in cancer. However, much less is known about the contribution of RNA Binding Proteins (RBPs) to this process. RBPs are the key orchestrators of gene regulation at the post-transcriptional level and are essential for defining the final transcript repertoire in a cell.
In the proposed project, the selected candidate will work in developing new computational tools to define gene regulatory networks (GRNs) controlled by RBPs and characterize their dynamics and function in the establishment of cell identity at the single-cell level. For this purpose, she/he would characterize GRNs in single-cell transcriptomics data and evaluate 1) how GRNs change during cell differentiation and 2) how these GRNs are altered in Alzheimer’s Disease. This work will require both the development of new computational tools for the prediction of GRNs as well as data mining and analysis skills to integrate data from different high-throughput and omics technologies for the identification of RBP target genes. For this purpose, the candidate will join a multidisciplinary team and work in close collaborations with other computational and experimental researchers contributing to the project.
We are seeking for a motivated and skilled PhD student with background in Computational Biology, Bioinformatics or similar with strong statistics and programming skills. The Plass Group offers a highly dynamic, multi-national, and intellectually stimulating working environment with cutting-edge techniques such as single-cell transcriptomics, human pluripotent stem cells and genome editing. The PhD candidate will also have the opportunity to perform internships in external laboratories in the fields of computational biology or single-cell transcriptomics.
Email Dr. Plass for further details.